5HIX

Cocrystal structure of an anti-parallel DNA G-quadruplex and a tetra-Quinoline Foldamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.231 

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Ligand Structure Quality Assessment 


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Literature

Multivalent Interactions between an Aromatic Helical Foldamer and a DNA G-Quadruplex in the Solid State.

Mandal, P.K.Baptiste, B.Langlois d'Estaintot, B.Kauffmann, B.Huc, I.

(2016) Chembiochem 17: 1911-1914

  • DOI: 10.1002/cbic.201600281
  • Primary Citation of Related Structures:  
    5HIX

  • PubMed Abstract: 
  • Quinoline-based oligoamide foldamers have been identified as a potent class of ligands for G-quadruplex DNA. Their helical structure is thought to target G-quadruplex loops or grooves and not G-tetrads. We report a co-crystal structure of the antiparallel hairpin dimeric DNA G-quadruplex (G 4 T 4 G 4 ) 2 with tetramer 1-a helically folded oligo-quinolinecarboxamide bearing cationic side chains-that is consistent with this hypothesis ...

    Quinoline-based oligoamide foldamers have been identified as a potent class of ligands for G-quadruplex DNA. Their helical structure is thought to target G-quadruplex loops or grooves and not G-tetrads. We report a co-crystal structure of the antiparallel hairpin dimeric DNA G-quadruplex (G 4 T 4 G 4 ) 2 with tetramer 1-a helically folded oligo-quinolinecarboxamide bearing cationic side chains-that is consistent with this hypothesis. Multivalent foldamer-DNA interactions that modify the packing of (G 4 T 4 G 4 ) 2 in the solid state are observed.


    Organizational Affiliation

    Bordeaux Institut National Polytechnique, CBMN, UMR 5248), 2 rue Escarpit, 33600, Pessac, France. i.huc@iecb.u-bordeaux.fr.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    Dimeric G-quadruplexA, B12synthetic construct
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    61Q (Subject of Investigation/LOI)
    Query on 61Q

    Download Ideal Coordinates CCD File 
    G [auth A]4-(3-aminopropoxy)-8-({[4-(3-aminopropoxy)-8-({[4-(3-aminopropoxy)-8-({[4-(3-aminopropoxy)-8-nitroquinolin-2-yl]carbonyl}amino)quinolin-2-yl]carbonyl}amino)quinolin-2-yl]carbonyl}amino)quinoline-2-carboxylic acid
    C52 H52 N12 O11
    PDPDTUNURBJNEI-UHFFFAOYSA-N
     Ligand Interaction
    K
    Query on K

    Download Ideal Coordinates CCD File 
    C [auth A], D [auth A], E [auth A], F [auth A]POTASSIUM ION
    K
    NPYPAHLBTDXSSS-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.48 Å
    • R-Value Free: 0.288 
    • R-Value Work: 0.227 
    • R-Value Observed: 0.231 
    • Space Group: P 41
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 31.701α = 90
    b = 31.701β = 90
    c = 97.373γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement
    XDSdata reduction
    XDSdata scaling
    AMoREphasing

    Structure Validation

    View Full Validation Report



    Ligand Structure Quality Assessment  



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    European Research CouncilFranceERC-2012-AdG-320892

    Revision History  (Full details and data files)

    • Version 1.0: 2016-11-02
      Type: Initial release